view subsearch/subsearch.xml @ 0:527ecd2fc500 draft

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<tool id="ctb_subsearch" name="Substructure Search" version="0.1">
    <description>of fingerprint data sets</description>
    <requirements>
        <requirement type="package" version="2.3.2">openbabel</requirement>
    </requirements>
    <command interpreter="python">

    subsearch.py
        -i $query
        --iformat "${query.ext}"
        --fastsearch-index "${os.path.join($fastsearch.extra_files_path,'molecule.fs')}"
        -o "${outfile}"
        --oformat $oformat
        --max-candidates $max_candidates
        --processors 10

    </command>
    <inputs>
        <param name="query" type='data' format="tabular,smi,sdf,inchi,text" label="query"/>
        <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index"/>
        <param name="max_candidates" size="6" type="integer" value="4000" label="The maximum number of candidates"/>
        <param name='oformat' type='select' format='text' label="Output format.">
            <option value='smi'>SMILES</option>
            <option value='inchi'>InChI</option>
            <option value='sdf'>SD-Files</option>
            <option value='mol2'>mol2</option>
            <option value='names'>Return the molecule names only</option>
        </param>
    </inputs>
    <outputs>
       <data format="smi" name="outfile">
         <change_format>
           <when input="oformat" value="inchi" format="inchi"/>
           <when input="oformat" value="sdf" format="sdf"/>
           <when input="oformat" value="mol2" format="mol2"/>
           <when input="oformat" value="names" format="tabular"/>
         </change_format>
       </data>
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help>

.. class:: infomark

**What this tool does**

Substructure search in based on Open Babel FastSearch_ Index. It uses molecular fingerprints to prepare and search an index of a multi-molecule datafile.

.. _FastSearch: http://openbabel.org/wiki/FastSearch

-----

.. class:: infomark

**Input**

SMILES or SMARTS patterns are possible. SD- and InChI files are converted to SMILES.

-----

.. class:: infomark

**Cite**

`Open Babel`_

.. _Open Babel: http://openbabel.org/wiki/Main_Page

    </help>
</tool>